Genetic diversity of bovine coronaviruses from recurrent outbreaks on a large-scale cattle farm

This study aimed to characterize the molecular features of bovine coronavirus (BCoV) outbreaks detected on a large-scale cattle farm in Türkiye during three respiratory outbreaks (January, May, and August 2024). Respiratory outbreaks were recorded in all three periods, with the August outbreak also being associated with enteric infection. A total of 52 samples (42 nasal samples and 10 fecal samples) were analyzed using RT-nested PCR targeting the N gene, and 13 samples (12 nasal samples and one fecal sample) tested positive. Among six partial N gene sequences that could be obtained from the outbreak in January ( n = 1) and August ( n = 5), two sequences from the August outbreak exhibited a three–amino acid deletion in the RS/SR domain. Furthermore, partial S gene sequences from two samples from the January and August outbreaks revealed different amino acid substitutions. The observed genetic variations indicate the presence of genetically distinct BCoV strains detected during different outbreak events on the farm and support the need for sustained molecular surveillance in cattle farming systems.